Single nucleotide polymorphisms, environmental data and R scripts used in the work: A donor registry: Genomic analyses of Posidonia australis seagrass meadows identifies adaptive genotypes for future-proofing

Globally, anthropogenic climate change has caused declines of seagrass ecosystems necessitating proactive restoration approaches which would ideally anticipate future conditions. In eastern Australia, environmental conditions in estuaries with meadows of the endangered seagrass Posidonia australis have warmed and acidified over the past decade and seagrass communities have declined in some estuaries. Securing these valuable habitats will require proactive conservation and restoration efforts that could be augmented with restoration focussed on boosting resilience to future change.  Understanding patterns of selection and where seagrass meadows are adapted to particular environmental conditions is key for identifying optimal donor material for restoration. We use single nucleotide polymorphisms and genotype by environment analyses to identify candidate loci under putative selection to environmental stressors and assess genomic variation and allelic turnover along stressor gradients. The ..., A total of 342 individual P. australis were initially genotyped with the DArTseq™ platform yielding a total of 11,382 SNP loci with a mean read depth of 7.07 and 20.73% missing data. Sequencing error was estimated by calculating the maximum proportion of allelic differences (bitwise distance) found between six pairs of technical replicates using bitwise.dist in the R package poppr which was used as a threshold. No sequencing errors were detected and technical replicates were then removed from the dataset. To enhance the quality of SNPs and to optimise the number of loci available for identification of candidate SNPs under potential selection, a data filtering strategy was employed using several functions in the R package dartR v.2.7.2. Data were filtered applying a locus call rate of 0.67, and individual call rate of 0.25 and a reproducibility threshold of 0.99. Read depth filter parameters were set at 2 to 50 and SNPs were thinned by setting the MAF to default (0.01). After filtering, ..., , # Single nucleotide polymorphisms, environmental data and R scripts used in the work: A donor registry: Genomic analyses of Posidonia australis seagrass meadows identifies adaptive genotypes for future-proofing

[https://doi.org/10.5061/dryad.d2547d89s](https://doi.org/10.5061/dryad.d2547d89s)

## Description of the data and file structure

We used single nucleotide polymorphisms (SNP data provded here) and genotype by environment analyses (environmental data provided here) to identify candidate loci under putative selection to environmental stressors and assess genomic variation and allelic turnover along stressor gradients for the seagrass Posidonia australis in estuaries along the New South Wales (Australia) coast.

### Files and variables

#### File: PosidoniafiltereddataGEASNPs.csv

**Description:** DArT Sequence generated single nucleotide polymorphisms for individual loci from multiple individuals

##### Variables

* Individual: Samples from estauries in New South Wales - see est...

全球范围内，人为活动引发的气候变化已导致海草生态系统衰退，亟需采取前瞻性修复策略，理想情况下应能预判未来环境变化。在澳大利亚东部，分布有濒危海草澳洲波喜多草（Posidonia australis）草床的河口环境，在过去十年间已出现增温和酸化现象，部分河口的海草群落已出现衰退。保护这些极具价值的生境，需要前瞻性的保护与修复工作，而聚焦于提升生态系统对未来变化适应力的修复手段可进一步强化这一成效。明确选择模式以及海草草床对特定环境条件的适应位点，是筛选最优修复供体材料的关键。本研究借助单核苷酸多态性（single nucleotide polymorphisms, SNP）与基因型-环境关联分析，识别出潜在受环境胁迫选择的候选位点，并评估了沿胁迫梯度的基因组变异与等位基因更替情况。……本研究最初利用DArTseq™平台对342株澳洲波喜多草个体进行基因分型，共获得11382个SNP位点，平均测序深度为7.07，缺失数据占比20.73%。测序误差通过R包poppr中的bitwise.dist函数计算6对技术重复样本间的最大等位基因差异比例（位距距离）进行估算，并以此作为阈值。经检测未发现测序误差，随后将技术重复样本从数据集中移除。为提升SNP数据质量并优化潜在选择候选SNP位点的筛选可用位点数量，本研究采用R包dartR v.2.7.2中的多项函数开展数据过滤：设置位点检出率阈值为0.67、个体检出率阈值为0.25、重现性阈值为0.99；读取深度过滤参数设置为2至50；并将最小等位基因频率（minor allele frequency, MAF）设为默认值0.01以进行SNP位点稀疏化。过滤完成后，……本研究相关的单核苷酸多态性数据、环境数据及R脚本已公开：供体登记库：澳洲波喜多草草床的基因组分析可识别可支撑未来修复的适应性基因型
https://doi.org/10.5061/dryad.d2547d89s

### 数据与文件结构说明
本研究借助单核苷酸多态性（即本数据集提供的SNP数据）与基因型-环境关联分析（环境数据亦随本数据集提供），针对澳大利亚新南威尔士州沿岸河口的澳洲波喜多草，识别潜在受环境胁迫选择的候选位点，并评估沿胁迫梯度的基因组变异与等位基因更替情况。

#### 文件与变量
##### 文件：PosidoniafiltereddataGEASNPs.csv
**描述**：通过DArT序列技术生成的多个体单核苷酸多态性位点数据
##### 变量
* Individual：取自新南威尔士州河口的样本——详见河口……